geom_msa.Rd
Multiple sequence alignment layer for ggplot2. It creats background tiles with/without sequence characters.
geom_msa( data, font = "helvetical", mapping = NULL, color = "Chemistry_AA", custom_color = NULL, char_width = 0.9, none_bg = FALSE, by_conservation = FALSE, posHighligthed = NULL, seq_name = NULL, border = NULL, consensus_views = FALSE, use_dot = FALSE, disagreement = TRUE, ignore_gaps = FALSE, ref = NULL, position = "identity", show.legend = FALSE, ... )
data | sequence alignment with data frame, generated by tidy_msa(). |
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font | font families, possible values are 'helvetical', 'mono', and 'DroidSansMono', 'TimesNewRoman'. Defaults is 'helvetical'. |
mapping | aes mapping If font = NULL, only plot the background tile. |
color | A Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER','CN6',, 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'. Defaults is 'Chemistry_AA'. |
custom_color | A data frame with two cloumn called "names" and "color".Customize the color scheme. |
char_width | a numeric vector. Specifying the character width in the range of 0 to 1. Defaults is 0.9. |
none_bg | a logical value indicating whether background should be disaplayed. Defaults is FALSE. |
by_conservation | a logical value. The most conserved regions have the brightest colors. |
posHighligthed | A numeric vector of the position that need to be highlighted. |
seq_name | a logical value indicating whether seqence names should be displayed. Defaults is 'NULL' which indicates that the sequence name is displayed when 'font = null', but 'font = char' will not be displayed. If 'seq_name = TRUE' the sequence name will be displayed in any case. If 'seq_name = FALSE' the sequence name will not be displayed under any circumstances. |
border | a character string. The border color. |
consensus_views | a logical value that opeaning consensus views. |
use_dot | a logical value. Displays characters as dots instead of fading their color in the consensus view. |
disagreement | a logical value. Displays characters that disagreememt to consensus(excludes ambiguous disagreements). |
ignore_gaps | a logical value. When selected TRUE, gaps in column are treated as if that row didn't exist. |
ref | a character string. Specifying the reference sequence which should be one of input sequences when 'consensus_views' is TRUE. |
position | Position adjustment, either as a string, or the result of a call to a position adjustment function, default is 'identity' meaning 'position_identity()'. |
show.legend | logical. Should this layer be included in the legends? |
... | additional parameter |
A list
Guangchuang Yu, Lang Zhou seq_name' work posHighligthed' work border' work none_bg' work
library(ggplot2) aln <- system.file("extdata", "sample.fasta", package = "ggmsa") tidy_aln <- tidy_msa(aln, start = 150, end = 170) ggplot() + geom_msa(data = tidy_aln, font = NULL) + coord_fixed()